Ive got a 600w HPS in a closet (getting a 250 this weekend) and the temps are barely controllable, what I have to do is have my window all the way open and my door closed, and also the radiator off in my room.
And yep, take the temps where the top of the plants are. You can take the temps at the bottom aswell as the top, just for peace of mind, but I really dont think that the temperature will differ more than a couple of degrees from the top and the bottom. It puts your mind at rest though.